It seems that my solution wasn't perfect afterall, because it breaks Bamboo's change detection. I would file an issue about this, but your Jira seems to be down at the moment. So I'll describe it here and create the issue later.

The problem is propably related to a CVS bug described here:
http://ximbiot.com/cvs/manual/cvs-1.11.22/cvs_18.html#SEC162

I have multiple modules under CVS root grouped under one ampersand module called "orgh". The modules -file looks like this.
orgh &OrgHallintaPOM &OrgHallinta &OrgHallintaAPI &OrgHallintaEntityEJB ....

When I make change in OrgHallintaPOM/pom.xml, Bamboo tries to execute command "cvs log -N -r -d>2007-02-02 13:41:01 pom.xml" in orgh -directory instead of orgh/OrgHallintaPOM -directory.

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INFO:
Running CVS command: 'update -d -P '<br />
... in: 'D:/bamboo/xml-data/build-dir/ORGHAL-CI/orgh'
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\build-number.txt
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallinta\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaAPI\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaEntityEJB\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaJava\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaPanWeb\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaPersistenssi\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaSamWeb\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaSessionEJB\target
2007-02-02 13:50:46,474 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaTehtavanHallinta\target
2007-02-02 13:50:46,646 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] ? Directory D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaTest\target
2007-02-02 13:50:47,583 INFO [BAM::BuildChangeDetector] [CvsUpdateLogListener] U D:\bamboo\xml-data\build-dir\ORGHAL-CI\orgh\OrgHallintaPOM\pom.xml
2.2.2007 13:50:48 com.atlassian.bamboo.repository.cvsimpl.CVSRepository getChangesFromCommand
INFO: Found 1 changes from update
2.2.2007 13:50:48 com.atlassian.bamboo.repository.cvsimpl.CVSRepository getChangeLogs
INFO: Running CVS log command: "log -N -r -d>2007-02-02 13:41:01 pom.xml "
2.2.2007 13:50:48 com.atlassian.bamboo.repository.cvsimpl.CVSRepository getChangeLogs
INFO: ... in: "D:/bamboo/xml-data/build-dir/ORGHAL-CI/orgh"
2.2.2007 13:50:48 com.atlassian.bamboo.repository.cvsimpl.CVSRepository getChangeLogs
INFO: Found 0 changes sets in the change logs
2.2.2007 13:50:48 com.atlassian.bamboo.repository.cvsimpl.CVSRepository collectModuleChanges
INFO: something wrong with the change logs, so lets work out what's changed...
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Is this something you can have fixed before the 1.0 release? I think many Eclipse and IBM RAD users with CVS are affected by this because this repository layout seems to be the default with these tools.

The alternative workaround is not acceptable for us, because we are setting up a shared build environment for multiple projects and this aproach would generate hundreds of build plans.

Having to use the modules -file is a bit hackish anyway and better solution would of course be to allow multiple modules under one plan. If branch or tag could be defined individually for the modules, this could be used for some configuration management too.